4 turn research, allows workers to transform into a basic pikeman unit. The idea is to have workers able to be conscripted into the army, and given a spear, which is one of the simplest weapons to teach. It allows for a fast defense if the enemy gets too close, but comes at the cost of 1. your workers can't build anymore and 2. It takes 3 turns to make a worker while it takes 2 turns to make a pikeman, meaning you actually lost a production turn by doing this. This would allow human players more freedom to hurry up and build without worrying as much about worker safety, as a threatened worker just turns into military, and once everything is built the player they can use the excess workers without giving them busy work making more and more towers.

Currently residing at the local ninja academy. I'm still watching though.

Honestly I'm not sure if there is a need for Vanishing. The worker cost 3 turns in a TC to build, when the same TC could have made a pikeman in 2 turns, so 33% less cost to just make the military unit from the start. And that isn't counting the research time, also taken out of a TC that could be making military from the start. It simply isn't cost efficient. True, workers can make up that by making siege equipment and towers or factory buildings before being conscripted, but this probably just evens it out in the end.

Currently residing at the local ninja academy. I'm still watching though.

What about a reversible effect? You press the skill button and the workers becomes a weak unit (in between swordman and pikeman but with lower bonuses) but can't build anymore. If you press the skill again it is turned back into a worker